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Status
PPD_0039B9J.1
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Download FASTA
Download metadata TSV
Display Name: Pakistan/PPD_0039B9J.1/2023-08-26
Umair,
M.; Haider,
S. A.; Jamal,
Z.; Ammar,
M.; Hakim,
R.; Ali,
Q.; Salman,
M.
Submission details
Submission ID
OR964926.1.L/OR964937.1.M/OR964915.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2024-11-19 16:17:00 UTC
Date released
2024-11-19 16:30:17 UTC
Data use terms
Data use terms
OPEN
✕
Data Use Terms History
Changed
User
Data Use Terms
2024-11-19 16:17
insdc_ingest_user
OPEN
Close
(history)
Data use terms URL
https://pathoplexus.org/about/terms-of-use/open-data
Authors
Author affiliations
National Institute of Health, Department of Virology
Alignment states and QC metrics L
Completeness L
96.90%
Length L
12094
Total ambiguous nucs L
0
Total deleted nucs L
13
Total frame shifts L
0
Total inserted nucs L
33
Total SNPs L
1410
Total unknown nucs L
341
Alignment states and QC metrics M
Completeness M
96.76%
Length M
5258
Total ambiguous nucs M
0
Total deleted nucs M
0
Total frame shifts M
0
Total inserted nucs M
1
Total SNPs M
618
Total unknown nucs M
65
Alignment states and QC metrics S
Completeness S
95.93%
Length S
1591
Total ambiguous nucs S
0
Total deleted nucs S
50
Total frame shifts S
0
Total inserted nucs S
4
Total SNPs S
191
Total unknown nucs S
33
Sample details
Collection country
Pakistan
Collection date
2023-08-26
Isolate name
CCHF/NIHPAK-19/2023
Host
Host name scientific
Homo sapiens
Host taxon id
9606
INSDC
INSDC accession L
OR964926.1
INSDC accession M
OR964937.1
INSDC accession S
OR964915.1
NCBI release date
2023-12-26
Nucleotide mutations
Substitutions
L
L:
G
32
A
L:
A
35
G
L:
T
49
C
L:
T
61
G
L:
T
67
A
L:
G
69
T
L:
G
88
A
L:
G
93
A
L:
A
109
G
L:
G
119
A
L:
A
124
G
L:
T
131
A
L:
C
136
T
L:
T
139
C
L:
C
145
T
L:
C
148
T
L:
T
151
C
L:
T
160
C
Show more
M
M:
C
82
T
M:
C
85
T
M:
T
86
C
M:
A
107
G
M:
A
117
G
M:
C
119
T
M:
C
120
T
M:
T
122
C
M:
C
126
T
M:
A
128
G
M:
T
137
C
M:
G
143
A
M:
A
146
G
M:
G
147
A
M:
G
149
A
M:
C
153
A
M:
T
155
C
M:
T
159
C
Show more
S
S:
A
50
G
S:
G
54
A
S:
G
67
A
S:
T
79
C
S:
G
99
A
S:
G
100
A
S:
A
109
G
S:
A
118
G
S:
C
142
T
S:
C
166
T
S:
G
169
A
S:
T
172
C
S:
C
178
A
S:
T
182
C
S:
T
199
C
S:
C
217
T
S:
G
229
A
S:
A
268
C
Show more
Deletions
L:70, L:71, L:11918-11920, L:11981, L:11982, L:12028, L:12034, L:12035, L:12073, L:12088, L:12089, S:1541-1543, S:1614-1660
Insertions
ins_S:1530:TNC, ins_S:1577:A, ins_M:5166:G, ins_L:12063:C, ins_L:12096:GCTC, ins_L:12079:C, ins_L:11924:NTCTG, ins_L:58:TCT, ins_L:11977:A, ins_L:11973:A, ins_L:12053:CTACAATGTTTTCAGCT
Amino acid mutations
Substitutions
GPC
GPC:
I
9
V
GPC:
L
10
F
GPC:
E
19
K
GPC:
H
21
N
GPC:
S
23
L
GPC:
E
26
G
GPC:
R
28
E
GPC:
D
33
H
GPC:
T
34
V
GPC:
G
39
D
GPC:
N
41
S
GPC:
P
42
Q
GPC:
S
44
P
GPC:
S
53
P
GPC:
I
54
V
GPC:
L
56
P
GPC:
Y
77
H
GPC:
P
80
S
Show more
NP
NP:
R
15
K
NP:
V
83
A
NP:
D
116
E
NP:
T
124
S
NP:
G
125
N
NP:
H
195
R
NP:
D
199
E
NP:
I
246
V
NP:
V
254
I
NP:
R
270
K
NP:
S
301
G
NP:
A
307
V
NP:
Q
405
L
NP:
V
436
I
RdRp
RdRp:
S
6
N
RdRp:
G
15
S
RdRp:
S
19
T
RdRp:
Y
60
N
RdRp:
R
63
H
RdRp:
S
67
V
RdRp:
R
80
K
RdRp:
V
82
I
RdRp:
T
163
A
RdRp:
M
172
V
RdRp:
S
205
P
RdRp:
K
275
R
RdRp:
I
279
V
RdRp:
S
498
G
RdRp:
I
505
T
RdRp:
A
508
V
RdRp:
K
522
R
RdRp:
T
720
S
Show more
Deletions
None
Insertions
None
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